Chuck Vs The Past
by river1234
Summary: This is an alternate storyline to Chuck ep 23 of Season 4. It mostly focuses on the relationship between Orion, Mary and Hartley. It also includes their backstory which i changed/extended a bit. Their story is so interesting so I hope you enjoy what i came up with:)
**Chuck versus the Past**

 **About this fanfic:**

I used a lot from episode 23 of Season 4 (I guess you could say it is an alternate episode to that one) but wanted to get a lot deeper into the relationship between Orion, Mary and Hartley/Volkoff as I always thought there was more of a story behind their lives than was shown in Season 4, which i think neglected a lot. (and missed many opportunities like getting Scott Bakula back for flashbacks with Linda Hamilton:) Most of Chuck's parents' back story is taken directly from the series, however I changed some things or simply added more detail (since we know so little about it): For example Orion knows here where Mary is going (Volkoff) when she leaves home – I always thought it was stupid that Orion was trying to „find" her. In my head, Orion and Mary were working together to both fix Hartley and bring his network down, which Chuck indicated in episode 22 of Season 4 when he said that maybe Mary was trying to „fix him too but in her own way." I also thought about adding something about Vivian being Mary's daughter (since Volkoff is in love with her and we don't know her mom), and therefore Chuck's half sister, but i thought it was too weird.

 **A quick summary of Mary and Orion's Backstory (including some things i made up to make it more interesting, they're italicized):**

Hartley is Steven's best friend and Mary also considers him a close friend. When Steven's Intersect prototype changes Hartley's personality and causes him to mistake himself for someone else and use his inserted personality's knowledge and power to become a powerful armsdealer, Mary and Orion decide to help him by turning him back into who he really is. When Mary gets involved in a project to take Volkoff Industries down at its early stages, she gets in too deep and has to disappear. _Orion begs her to stay and find another solution, but ultimatively accepts Mary has left and tries to develop a special supression device to try and surpress the broken intersect's data and erase the current flaw or virus running through the programme, as well as making Hartley remember his life while his own memories are being uploaded into his brain._ However, when Mary does not return after several years, he decides to leave home because he cannot bear the thought of Mary and Hartley being lost without his help and deciding that he would hide from the CIA in order to protect himself and his children and cover up the Agent X affair for as long as Hartley remains Volkoff and beyond.

 **Flashback Scene (Encino, 1980)**

Mary opens the door with a tray in her hands, two cups of tea on it. Her husband and Hartley Winterbottom are sitting in front of the computer, discussing and working.

„There you go, boys", Mary says in a calm, motherly voice, putting the tray on an unused chair besides the two men. „You two have been working all evening. You've got to be tired."

„It's okay honey, we'll quit in a few hours."

„What's so exciting anyway?", she asks. But Steven and Hartley are so deep into their work that they don't even notice.

Mary sighs, then starts humming as she walks out the door.

„You know, Hartley..er, I've been working on this project that has been keeping me occupied for quite some time now. Maybe you could help me develop it?"

„What would I do?"

„It'd just be some testing. But i need your opinion. See, you're the greatest scientist I know, and this project, it's called the Intersect."

 **Echo Park, Los Angeles, 2010 (Present)  
**

Chuck and Sarah tried to focus on the wedding. Until Casey showed up at the door.

„Casey, don't...", said Sarah.

„no, no, no no no wait this is not for a mission is it? Please please say it's not for a mission..." Chuck begged.

„Listen", he said, „It's about your mom. She's gone. Vivian Volkoff has taken her in."

„What?", said Chuck. „How could this happen?"

„It doesn't matter, Chuck. We need to go to Castle and figure out a move. Let's go." Chuck and Sarah followed.

„Ok, let's think about this, what would my mom do at Volkoff's headquarters two days before our wedding? What's gotten into her?"

„Chuck, calm down", said Sarah.

He sat down impatiently.

„Do you think this is about Agent X?", Sarah said.

„Whatever it is, we need to go there and find out", said Casey.

„We can't just waltz in there, we have a wedding to prepare."

„Do you have any ideas?", asked Casey.

 **At Volkoff Industries (Present)  
**

In the meantime, Mary was sitting in her cell, impatiently waiting as Vivian approached.

„What were you looking for back there? What's your identity? And don't lie to me," she said, reaching for her gun.

„Good", said Riley as he approached, having watched from afar. Vivian hesitated a little before grabbing the gun, but in Riley's presence she was confident she could take the shot if she had to.

„Frost is a traitor. She betrayed your father for 20 years posing as his right arm when all she was was a fool, thinking she could bring down your father's network that he has so carefully built up. Don't you want to eliminate her? Don't you think she's a pain in the ass? Go ahead, do it!"

„How do I know this is true?", Vivian said, still hesitating.

„Because..."

„Freeze!", yelled Sarah, surrounded by Chuck and Casey.

„What have we here? Guess you Bartowskis just won't let off of each other," said Riley.

„Chuck!", yelled Mary.

„Mom, are you okay?"

„Mom? Your mother betrayed my father, and you betrayed me? Well, I should have seen that coming...", said Vivian.

„Vivian, listen, you have to let her go. She's innocent. Your father isn't who you think he is, he used to be a scientist, his real name is Hartley, and he let the CIA perform an experiment on him that made him into who he is."

„Riley is this true?"

„Yes, yes it is. But it was his father that turned him, Steven J. Bartowski. Him and Frost used him, they wanted him to give up his career to improve theirs! Now take what's yours Vivian, I know you want it!"

Vivian's hands shook as she was about to shoot Mary, but couldn't do it.

„Alright then, if you're not gonna take it, then I am." Riley wanted to go ahead but Sarah shot him instead.

Vivian screamed.

„Vivan, listen. Your father, Hartley, he was a friend of mine and Steven all those years ago. When my husband developed the Intersect, Hartley agreed to be used as a test object. He was excited to use the intersect on a mission. Steven didn't approve at first as he thought the programme needed more work. He didn't know what side effects it could have. Since then, we have done everything we could to turn your father back into who he really is. That's why I am here."

„I can't believe this. If you're saying the truth then why didn't you try to fix him earlier?"

„I did. We both did. With Chuck finding out about Agent X, I decided I didn't want to take any more risks and finally eliminate Volkoff, get back our friend. I kept one thing from Steven's base that I knew someday I would have use for it. A special surpression device he created several years before his death. It was supposed to restore Hartley's memories and allow him to take control of himself, as well as surpress the flawed intersect. When Volkoff saw me with it, he took it and has since stored it somewhere where even I haven't been able to find it in all these years. I told him it was a dangerous weapon that only Steven knew how to operate, a weapon that we could make use of. But he mistrusted me back then, even more so than now. Steven knew that I was out to do the same that he was all those years ago, but I didn't dare pushing my husband into this knowing what Volkoff was capable of and after 10 years, this had become my life. Knowing your father", she said looking over to Chuck, „he left you at the point when I got in way too deep – to assist me, but most importantly, to protect you. But obviously, he never was able to accomplish what he'd hoped for so much. I wanted to fix him, but I knew I had to bring his network down first. That was my part. I was hoping I could finally give Hartley back what he deserves after all of this, now that Steven is dead. So here I am."

 **Flashback Scene (Encino 1994)**

Mary is working at her safe place beneath the Bartowski family home one day when she gets a call. „We have to move you. Now", a voice says on the phone. They want her to disappear from the radar for a while. Guarantee her safety. But Mary realizes there is no safety anymore – neither for her nor her family. Volkoff's men are probably on their way to her. Mary doesn't have time to figure out what to take and what not. She grabs a few guns and weapons which she hides all over her body. She sees a picture of Chuck and Ellie, and for a second she thinks about taking it with her. She hesitates. This is taking too long. „No", she says to herself, putting down the picture. She knows her family can be used against her. „Goodbye", she whispers, allowing herself one more glance at the photo. Did she really just read a goodnight story to Chuck a few minutes ago? They are here. Orion walks into her safehouse, grabs her cheeks and says:

„It doesn't have to be like this. Please, Mary, don't go. We can find a way!"

„You know it has to be this way, honey, I'm sorry. I love you."

As they hear Volkoff's men drawing near, Orion gives Mary a kiss and Mary locks him inside, walking out as Orion is screaming, calling for her.

 **Flashback Scene 2 (Volkoff Industries, 1994)**

Upon her forced arrival at his headquarters, Mary requests a meet with Volkoff, so she is brought into his office by his men.

"Mr. Volkoff, this is Mary Bartowski from the CIA. She was one of the agents in charge of Project ISIS."

"I see", he says with a smile on his face, recognizing her. "It's good you brought her to me. Even though I didn't ask for it."

"I requested to talk to you in person." Mary knows it would raise suspision if she stayed silent for too long.

"Your last mission was to take down my empire. Why would I listen to you? You've been compromised. The other agents who took part in this mission. Give me their names." Volkoff seems to be having a bad day.

"You don't understand, I.."

"Now", he says in a harsh voice, looking at one of his men who have their guns pointed at her head, then back to her.

Time to act. Mary takes out the three men surrounding her in a few swift movements. Then she points two of their guns at him.

"You will listen to me now. I took part in ISIS because I wanted to keep my cover within the agency. I've been preparing for my transfer through your men because I want to work with you."

"You _wanted_ to be found", he says, then pauses. "Clever move."

"Thank you. It was the only way I could gain your trust."

Volkoff smiles.

 **Back to Present (At Volkoff)**

It was hard not to believe this story as it was so weird and unique, and Vivian noticed how emotional Mary was throughout her telling it.

„What I'm saying is real, Vivian", she said. „Please, believe me." Vivian nodded. She had a confused look on her face, but she believed her.

„I happen to know the weapon you are talking about. At some point, Volkoff told me of its importance. He let me know where to find it."

Mary was led to Vivian's office. Vivian showed her the lockers where the weapon was supposed to be and she quickly found it – empty. Vivian's gun clicked behind Mary's head.

„If anything happens, I'll shoot you first," Sarah threatened.

„Vivian," Mary said, trembling, „someone is behind this. We're too late."

„Shut up! I don't believe a word you're saying. Eversince I met your family, I have been through nothing but lies and more lies and I can't take it anymore."

„Guys," a voice in the back said. It was Sarah. She had searched Riley for the weapon and returned with it. He'd had it in his pocket.

„I never trusted him with that", Vivian said.

„I don't know how he got this. But it must be the weapon my father described to me. Mary?"

Mary took it. „Do you have any idea for how long I have been looking for this?", she said.

„He was loyal to Volkoff", said Chuck. He must've taken it to prevent him being turned back into who he is."

„We have to find Hartley", Mary said.

 **At CIA Facility (Volkoff's Prison) (Present)  
**

They all rushed into the CIA facility where Volkoff was being held. They decided it was Mary who should turn Hartley back to normal.

„The Bartowskis. What a lovely surprise", he said in his usual, sarcastic tone.

„I don't believe.." he paused as Vivian walked in the room.

„We're not here to visit", Mary said. Mary looked over at Casey, nodding so he'd point his tranq gun at Volkoff as she unlocked his cell.

„What the.."

„We're here to fix you."

„Fix me? How would you fix me?"

„You're not this person, Alexei", she said. As she leaned forward, she whispered to him: „You deserve to be who you are."

Then she put the glasses on Volkoff.

After the images stopped, Hartley looked at Mary.

"Where have I been?", he said with tears in his eyes. Deep inside he knew.

"It doesn't matter. You're back", Mary said in a calm voice.

He embraced her. It was different than Volkoff, but it didn't feel like he was being a friend who needed comfort. Just like Volkoff, he was in love with her. She never understood – these have been _his_ feelings all along.


End file.
